D. Nelson Nov. 11, 1998
The figure above was created from an alignment of 77 bacterial P450s using Protdist (with PAM matrix option) Neighbor (with UPGMA option) and Drawgram from the Phylip package. 15 Mycobacterium tuberculosis genes are included. Five more are eukaryote like P450s and so they will be placed on a eukaryotic tree. The sequences CYP135, 136 and 137 at the bottom may also be eukaryote like sequences that belong on a eukaryote tree. Previous trees used for nomenclature purposes have been made using a scoring matrix that only counted identities rather than similarities like the PAM250 matrix.
This has caused some movement of the branches that is creating a problem in the nomenclature of the CYP105 and 107 families. Note that sequences from these families are mixed together in the top half of the tree. The unit matrix is useful because it computes percent identities for all sequence pairs in an alignment, but it may not produce the most accurate tree. Names for about 30 new P450 sequences will be assigned based on this tree, once questions about how to treat old names in the CYP105 and 107 families are resolved.